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2VPY
Asym. Unit
Info
Asym.Unit (425 KB)
Biol.Unit 1 (409 KB)
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(1)
Title
:
POLYSULFIDE REDUCTASE WITH BOUND QUINONE INHIBITOR, PENTACHLOROPHENOL (PCP)
Authors
:
M. Jormakka, K. Yokoyama, T. Yano, M. Tamakoshi, S. Akimoto, T. Shimamura, P. Curmi, S. Iwata
Date
:
09 Mar 08 (Deposition) - 10 Jun 08 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : A,B,C,E,F,G
Biol. Unit 1: A,B,C,E,F,G (1x)
Keywords
:
Oxidoreductase, Molybdopterin Guanine Dinucleotide, Iron-Sulfur, Metal-Binding, Molybdopterin, Integral Membrane Protein, Mgd, Mpt, Iron, Fe4S4, 4Fe-4S, Molybdenum, Iron Sulfur Cluster
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Jormakka, K. Yokoyama, T. Yano, M. Tamakoshi, S. Akimoto, T. Shimamura, P. Curmi, S. Iwata
Molecular Mechanism Of Energy Conservation In Polysulfide Respiration.
Nat. Struct. Mol. Biol. V. 15 730 2008
[
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Hetero Components
(4, 18)
Info
All Hetero Components
1a: 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,... (MGDa)
1b: 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,... (MGDb)
1c: 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,... (MGDc)
1d: 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,... (MGDd)
2a: MOLYBDENUM ATOM (MOa)
2b: MOLYBDENUM ATOM (MOb)
3a: PENTACHLOROPHENOL (PCIa)
3b: PENTACHLOROPHENOL (PCIb)
4a: IRON/SULFUR CLUSTER (SF4a)
4b: IRON/SULFUR CLUSTER (SF4b)
4c: IRON/SULFUR CLUSTER (SF4c)
4d: IRON/SULFUR CLUSTER (SF4d)
4e: IRON/SULFUR CLUSTER (SF4e)
4f: IRON/SULFUR CLUSTER (SF4f)
4g: IRON/SULFUR CLUSTER (SF4g)
4h: IRON/SULFUR CLUSTER (SF4h)
4i: IRON/SULFUR CLUSTER (SF4i)
4j: IRON/SULFUR CLUSTER (SF4j)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
MGD
4
Ligand/Ion
2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE
2
MO
2
Ligand/Ion
MOLYBDENUM ATOM
3
PCI
2
Ligand/Ion
PENTACHLOROPHENOL
4
SF4
10
Ligand/Ion
IRON/SULFUR CLUSTER
[
close Hetero Component info
]
Sites
(18, 18)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
CYS A:44 , CYS A:47 , CYS A:51 , CYS A:79 , ARG A:81 , GLY A:82 , ASN A:216
BINDING SITE FOR RESIDUE SF4 A1764
02
AC2
SOFTWARE
PHE A:48 , HIS A:145 , LEU A:172 , CYS A:173 , HIS A:333 , TYR A:438 , GLY A:439 , ILE A:440 , ASN A:441 , HIS A:444 , SER A:445 , ILE A:465 , ASP A:466 , GLN A:470 , HIS A:472 , GLU A:482 , ARG A:488 , TYR A:623 , ARG A:625 , PHE A:631 , ALA A:632 , ARG A:633 , HIS A:697 , ASP A:716 , ASN A:717 , GLN A:720 , MGD A:1766 , MO A:1767 , HOH A:2010 , HOH A:2384 , HOH A:2386
BINDING SITE FOR RESIDUE MGD A1765
03
AC3
SOFTWARE
ARG A:81 , CYS A:173 , GLY A:207 , HIS A:208 , HIS A:209 , GLU A:212 , ASP A:213 , THR A:214 , HIS A:215 , VAL A:235 , ASP A:236 , PRO A:237 , ARG A:238 , PRO A:254 , GLY A:255 , ASP A:257 , THR A:331 , ARG A:332 , HIS A:333 , TRP A:336 , TYR A:337 , ARG A:625 , SER A:626 , HIS A:629 , THR A:630 , PHE A:631 , ARG A:735 , MGD A:1765 , MO A:1767 , HOH A:2117
BINDING SITE FOR RESIDUE MGD A1766
04
AC4
SOFTWARE
CYS A:173 , MGD A:1765 , MGD A:1766
BINDING SITE FOR RESIDUE MO A1767
05
AC5
SOFTWARE
CYS B:13 , VAL B:14 , CYS B:16 , ALA B:18 , CYS B:19 , ILE B:38 , CYS B:135 , CYS B:139 , ARG B:140
BINDING SITE FOR RESIDUE SF4 B1194
06
AC6
SOFTWARE
CYS B:23 , ASN B:27 , LEU B:36 , GLN B:57 , CYS B:116 , THR B:117 , CYS B:119 , PRO B:129 , ALA B:130 , CYS B:131
BINDING SITE FOR RESIDUE SF4 B1195
07
AC7
SOFTWARE
CYS B:58 , LEU B:59 , HIS B:60 , CYS B:61 , PRO B:64 , CYS B:66 , VAL B:83 , CYS B:100 , ARG B:105 , LYS B:115
BINDING SITE FOR RESIDUE SF4 B1196
08
AC8
SOFTWARE
CYS B:70 , CYS B:90 , ILE B:91 , ALA B:92 , CYS B:93 , GLY B:94 , CYS B:96 , VAL B:113
BINDING SITE FOR RESIDUE SF4 B1197
09
AC9
SOFTWARE
CYS E:44 , CYS E:47 , TRP E:49 , ARG E:50 , CYS E:51 , CYS E:79 , ARG E:81 , GLY E:82 , ASN E:216
BINDING SITE FOR RESIDUE SF4 E1764
10
BC1
SOFTWARE
PHE E:48 , HIS E:145 , PRO E:168 , LEU E:172 , CYS E:173 , HIS E:333 , TYR E:438 , GLY E:439 , ILE E:440 , ASN E:441 , HIS E:444 , SER E:445 , ILE E:465 , ASP E:466 , HIS E:472 , GLU E:482 , ARG E:488 , TYR E:623 , ARG E:625 , PHE E:631 , ALA E:632 , ARG E:633 , HIS E:697 , ASP E:716 , ASN E:717 , GLN E:720 , MGD E:1766 , MO E:1767 , HOH E:2012 , HOH E:2396 , HOH E:2415 , HOH E:2449
BINDING SITE FOR RESIDUE MGD E1765
11
BC2
SOFTWARE
ARG E:81 , CYS E:173 , GLY E:207 , HIS E:208 , HIS E:209 , GLU E:212 , ASP E:213 , THR E:214 , HIS E:215 , VAL E:235 , ASP E:236 , PRO E:237 , ARG E:238 , PRO E:254 , GLY E:255 , ASP E:257 , THR E:331 , ARG E:332 , HIS E:333 , TRP E:336 , TYR E:337 , LEU E:622 , ARG E:625 , SER E:626 , PRO E:627 , HIS E:629 , THR E:630 , PHE E:631 , ARG E:735 , MGD E:1765 , MO E:1767 , HOH E:2131 , HOH E:2452
BINDING SITE FOR RESIDUE MGD E1766
12
BC3
SOFTWARE
CYS E:173 , MGD E:1765 , MGD E:1766 , HOH E:2217
BINDING SITE FOR RESIDUE MO E1767
13
BC4
SOFTWARE
CYS F:13 , VAL F:14 , GLY F:15 , CYS F:16 , CYS F:19 , ILE F:38 , PRO F:55 , CYS F:135 , CYS F:139 , ARG F:140
BINDING SITE FOR RESIDUE SF4 F1194
14
BC5
SOFTWARE
CYS F:23 , ASN F:27 , LEU F:36 , GLN F:57 , CYS F:116 , CYS F:119 , PRO F:129 , ALA F:130 , CYS F:131
BINDING SITE FOR RESIDUE SF4 F1195
15
BC6
SOFTWARE
CYS F:58 , LEU F:59 , CYS F:61 , PRO F:65 , CYS F:66 , VAL F:83 , CYS F:100 , TYR F:102 , ARG F:105
BINDING SITE FOR RESIDUE SF4 F1196
16
BC7
SOFTWARE
CYS F:70 , CYS F:90 , ILE F:91 , ALA F:92 , CYS F:93 , GLY F:94 , CYS F:96 , VAL F:113
BINDING SITE FOR RESIDUE SF4 F1197
17
BC8
SOFTWARE
ILE B:91 , CYS B:93 , HOH B:2078 , HIS C:21 , LEU C:64 , LEU C:79 , ILE C:89 , TYR C:130
BINDING SITE FOR RESIDUE PCI C1252
18
BC9
SOFTWARE
ILE F:91 , ASN G:17 , HIS G:20 , LEU G:63 , GLU G:66 , LEU G:78 , TYR G:129
BINDING SITE FOR RESIDUE PCI G1251
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
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Sorry, no Info available
[
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PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
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End label:
Sorry, no Info available
[
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]
Exons
(0, 0)
Info
All Exons
View:
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All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
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Label:
Sorry, no Info available
[
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CATH Domains
(7, 16)
Info
all CATH domains
1a: CATH_2vpyB01 (B:1-63,B:116-187)
1b: CATH_2vpyB02 (B:64-115)
1c: CATH_2vpyF02 (F:64-115)
1d: CATH_2vpyF01 (F:1-63,F:116-187)
2a: CATH_2vpyA04 (A:485-508,A:533-569)
2b: CATH_2vpyE04 (E:485-508,E:533-569)
3a: CATH_2vpyA03 (A:172-377,A:570-604)
3b: CATH_2vpyE03 (E:172-377,E:570-604)
4a: CATH_2vpyA02 (A:97-171,A:413-484,A:509-532)
4b: CATH_2vpyE02 (E:97-171,E:413-484,E:509-532)
5a: CATH_2vpyC00 (C:2-252)
5b: CATH_2vpyG00 (G:1-251)
6a: CATH_2vpyA05 (A:605-764)
6b: CATH_2vpyE05 (E:605-764)
7a: CATH_2vpyA01 (A:30-96)
7b: CATH_2vpyE01 (E:30-96)
View:
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Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Alpha-Beta Plaits
(1688)
Homologous Superfamily
:
[code=3.30.70.20, no name defined]
(120)
Thermus thermophilus. Organism_taxid: 262724. Strain: hb27. Thermus thermophilus. Organism_taxid: 262724. Strain: hb27.
(4)
1a
2vpyB01
B:1-63,B:116-187
1b
2vpyB02
B:64-115
1c
2vpyF02
F:64-115
1d
2vpyF01
F:1-63,F:116-187
Topology
:
Formate dehydrogenase/DMSO reductase,
(4)
Homologous Superfamily
:
Formate dehydrogenase/DMSO reductase,
(4)
Thermus thermophilus. Organism_taxid: 262724. Strain: hb27. Thermus thermophilus. Organism_taxid: 262724. Strain: hb27.
(4)
2a
2vpyA04
A:485-508,A:533-569
2b
2vpyE04
E:485-508,E:533-569
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Dimethylsulfoxide Reductase; domain 2
(37)
Homologous Superfamily
:
Dimethylsulfoxide Reductase, domain 2
(37)
Thermus thermophilus. Organism_taxid: 262724. Strain: hb27. Thermus thermophilus. Organism_taxid: 262724. Strain: hb27.
(4)
3a
2vpyA03
A:172-377,A:570-604
3b
2vpyE03
E:172-377,E:570-604
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
[code=3.40.50.740, no name defined]
(37)
Thermus thermophilus. Organism_taxid: 262724. Strain: hb27. Thermus thermophilus. Organism_taxid: 262724. Strain: hb27.
(4)
4a
2vpyA02
A:97-171,A:413-484,A:509-532
4b
2vpyE02
E:97-171,E:413-484,E:509-532
Class
:
Mainly Alpha
(13335)
Architecture
:
Up-down Bundle
(3216)
Topology
:
Formate dehydrogenase/DMSO reductase fold
(4)
Homologous Superfamily
:
Formate dehydrogenase/DMSO reductase domain
(4)
Thermus thermophilus. Organism_taxid: 262724. Strain: hb27. Thermus thermophilus. Organism_taxid: 262724. Strain: hb27.
(4)
5a
2vpyC00
C:2-252
5b
2vpyG00
G:1-251
Class
:
Mainly Beta
(13760)
Architecture
:
Beta Barrel
(4804)
Topology
:
Barwin-like endoglucanases
(75)
Homologous Superfamily
:
[code=2.40.40.20, no name defined]
(63)
Thermus thermophilus. Organism_taxid: 262724. Strain: hb27. Thermus thermophilus. Organism_taxid: 262724. Strain: hb27.
(4)
6a
2vpyA05
A:605-764
6b
2vpyE05
E:605-764
Architecture
:
Single Sheet
(341)
Topology
:
N-terminal domain of TfIIb
(166)
Homologous Superfamily
:
ADC-like domains
(18)
Thermus thermophilus. Organism_taxid: 262724. Strain: hb27. Thermus thermophilus. Organism_taxid: 262724. Strain: hb27.
(4)
7a
2vpyA01
A:30-96
7b
2vpyE01
E:30-96
[
close CATH info
]
Pfam Domains
(5, 10)
Info
all PFAM domains
1a: PFAM_Fer4_2vpyF01 (F:83-106)
1b: PFAM_Fer4_2vpyF02 (F:83-106)
2a: PFAM_Fer4_11_2vpyF03 (F:49-145)
2b: PFAM_Fer4_11_2vpyF04 (F:49-145)
3a: PFAM_Molydop_binding_2vpyE01 (E:619-738)
3b: PFAM_Molydop_binding_2vpyE02 (E:619-738)
4a: PFAM_Molybdop_Fe4S4_2vpyE03 (E:37-91)
4b: PFAM_Molybdop_Fe4S4_2vpyE04 (E:37-91)
5a: PFAM_Molybdopterin_2vpyE05 (E:94-528)
5b: PFAM_Molybdopterin_2vpyE06 (E:94-528)
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Clans
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)
(
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Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
4Fe-4S
(51)
Family
:
Fer4
(18)
Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
(4)
1a
Fer4-2vpyF01
F:83-106
1b
Fer4-2vpyF02
F:83-106
Family
:
Fer4_11
(12)
Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
(4)
2a
Fer4_11-2vpyF03
F:49-145
2b
Fer4_11-2vpyF04
F:49-145
Clan
:
AcetylDC-like
(37)
Family
:
Molydop_binding
(24)
Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
(4)
3a
Molydop_binding-2vpyE01
E:619-738
3b
Molydop_binding-2vpyE02
E:619-738
Clan
:
no clan defined [family: Molybdop_Fe4S4]
(17)
Family
:
Molybdop_Fe4S4
(17)
Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
(4)
4a
Molybdop_Fe4S4-2vpyE03
E:37-91
4b
Molybdop_Fe4S4-2vpyE04
E:37-91
Clan
:
no clan defined [family: Molybdopterin]
(24)
Family
:
Molybdopterin
(24)
Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
(4)
5a
Molybdopterin-2vpyE05
E:94-528
5b
Molybdopterin-2vpyE06
E:94-528
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